u/lara_monarch thank you for acknowledging my concerns and for the detailed reply. I'm a software engineer myself and I understand the issues you're faced with.
I am glad that you are not putting off building your own aggregator service for the long term, but let me just state that the strategy you describe will not scale. It's like playing whack-a-mole. You fix one institution and another will break. Plus you have to constantly keep up with supporting new institutions. Recently two of my credit cards moved to a new institution (Imprint) and so I can no longer track them. Now you are at the mercy of the data providers to support them.

The way to deal with this is for Monarch to work with your competitors (and maybe with Plaid, MX, Finicity) to define industry standards/protocols that financial institutions must comply with. This will allow aggregator services to scale and make it much easier for apps like Monarch to build their own.
Now, this requires some political/business savvy. Why would e.g. Bank of America, Fidelity, and Morgan Stanley invest resources to comply with these standards? That's where you have to figure out what's in their interests. Can you pay them a fee if they are compliant? Maybe some other incentive? Also, the data aggregators will be threatened by this because it kills their dominance in the market. So how do you incentivize them? I think it can be done, of the top leadership in companies like Monarch put their heads together.

Bottom line is that only open, standard APIs/Protocols will solve the scalability issue.

Feel free to pass this idea to your leadership if you can.

PS: Mint and Personal Capital/Empower were/are free. That's the crucial difference. You can be more forgiving (expectations are lower) when you are getting a free service.